Because they thought the elevens would buy it anyway, which they did.
I guess to save money, but Kyoani animated them all separately anyway, so they only saved on concept work and storyboarding and stuff, not animation.

I think that disappearance was meant to be in s2 but it got pulled at the last minute to to be made into a movie. So I'm guessing it was meant to take up 5-6 episodes and they had nothing else to run at that time.